Our system, called Pleiotropic Response Outputs from a Chemically-Inducible Single Receiver (PROCISiR), can be used to program diverse cellular responses owing to its single receiver protein architecture. Open Ned 19 in a separate window Fig. can be used to program diverse cellular responses, including graded and proportional dual-output control of transcription and mammalian cell signaling. We apply our tools to titrate the competing activities of the Rac and Rho GTPases to control cell morphology. Our receiver protein and suite of reader proteins provides researchers with a versatile toolset to post-translationally program mammalian cellular processes and to engineer cell therapies. Cells exhibit proportional, graded, digital and temporal behaviors in sensing and responding to multiple environmental or autologous inputs.1C3 Biologists seeking to reproduce natural functions, or produce new ones, need tools that can program a similar range of behaviors. Most reported synthetic biology tools are based on transcriptional circuits that can enable a wide variety of quantitative control modes.4,5 However, methods for rapid, protein-level manipulation of cellular processes have lagged Ned 19 behind due to the difficulty of engineering complex post-translational control schemes. For mammalian synthetic biology applications, post-translational control systems that use small molecules as extrinsic inputs are desirable for many applications because they are easy to use and and confer Ned 19 temporal modulation.6 Chemically-controlled proteases and degradation domains have been applied for post-translational control.7C9 Two recently-developed, chemically-controlled systems that use catalytically-active hepatitis C virus (HCV) protease NS3a as a cleavage-based modulator of mammalian cellular processes are particularly attractive because they use orally-available, clinically approved drugs that are orthogonal to mammalian systems as extrinsic inputs.10,11 Chemically-induced dimerization (CID) systems, which modulate cellular processes through small molecule-induced protein proximity, are advantageous for applications that require more rapid cellular responses, like cellular signaling, than protease- or Ned 19 degradation-based systems.12C14 Although there has been recent success in expanding the diversity of small molecules that can be used in CID systems, no system that uses a clinically-approved drug that lacks an endogenous mammalian target has been described to date.15 A limitation of current chemically-controlled systems is that they rely on single small molecule inputs that are translated into single outputs, which limits the types of cellular responses that can be programmed. There has been success in combining orthogonal CID systems to achieve digital logic control of cell signaling and transcription.14,16 In addition, combining composable, single-input/single-output protease-based systems has PRDI-BF1 allowed the assembly of a diversity of digital circuits.17 While digital logic is useful, current post-translational control systems lack robust analog outputs, such as graded and proportional control, that are needed to fully mimic natural cellular processes. Here, we present a new post-translational control system that utilizes the NS3a protease as a central receiver protein that is targeted by multiple clinically-approved drug inputs. To translate different drug-bound says of NS3a into diverse outputs, we engineer computationally-designed reader proteins that recognize specific inhibitor-bound says of NS3a and use a genetically-encoded peptide that selectively recognizes the form of this protease (Fig. 1a). Our system, called Pleiotropic Response Outputs from a Chemically-Inducible Single Receiver (PROCISiR), can be used to program diverse cellular responses owing to its single receiver protein architecture. Open in a separate windows Fig. 1 | Design of a danoprevir:NS3a complex reader.a, Schematic of the PROCISiR system. Multiple NS3a-targeting drugs are used as inputs that are interpreted by designed readers to generate multiple outputs. b, Goal and process for designing and optimizing drug:NS3a complex readers, starting from docking of several scaffold classes on a drug/NS3a complex, Rosetta design of the reader interface, filtering based on Rosetta interface scoring metrics, and finally testing and optimization via yeast surface display. c, Rosetta model for D5 (left) and binding of 1 1 M NS3a with avidity to yeast-displayed D5 in the presence or absence of 10 M danoprevir. A point mutant of the D5 interface, W177D, and the original DHR79 scaffold show no binding. Technical triplicates and means from one experiment. d, A co-crystal structure of the DNCR2:danoprevir:NS3a complex aligned with.